Global warming is changing the way the US trains for and goes to war – affecting war games, weapons systems, training exercises, and military installations – according to the Pentagon.

The defence secretary, Chuck Hagel, will tell a high-level meeting of military leaders on Monday that the Pentagon is undertaking sweeping changes to operation systems and installations to keep up with a growing threat of rising seas, droughts, and natural disasters caused by climate change.

“A changing climate will have real impacts on our military and the way it executes its missions,” Hagel wrote in his introduction to a Pentagon report out today. “We are considering the impacts of climate change in our war games and defence planning scenarios.”

But with Monday’s report, climate change moved from potential threat to an immediate factor in a wide range of operational and budgeting decisions.

“It makes it a reality that climate change indeed is a risk today, and we need to plan, programme and budget for it now and into the future,” said Sherri Goodman, chief executive of the military advisory board , a group of former generals and other high-ranking officers that studies US national security.

From now on, the military will factor climate change into a host of day-to-day decisions, a senior defence official told a conference call with reporters.

“It’s about being baked into things we are already doing, and incorporated into all the other things we are doing,” he said.

Those decisions could include war games, training exercises, and purchasing decisions – which could all be affected by conditions such as sea-level rise, heat waves, and drought.

War games scenarios would now factor in floods or storms instead of assuming optimal conditions, said Goodman. “You could make the game more complex with sea-level rise, and extreme weather events.”

She said the navy would have to test sonar and other systems under the changing ocean chemistry. The military will have to adapt to hotter temperatures.

One of the biggest and most costly decisions ahead is the location of some 7,000 US military sites.

As the report acknowledged, US military installations and personnel are already exposed to climate change. The Hampton Roads area in Virginia – which houses the biggest concentration of US forces – already floods during high tides and severe storms, and could see an additional 1.5 feet of sea level rise in the next 20 years.

Meanwhile, military bases in the south-west are coping with water and electricity shortages, under recurring droughts. Arctic land-based installations are shifting because of melting permafrost, while retreating sea ice is changing naval requirements.

The Pentagon is not planning a wholesale relocation of bases, the officials told the call. But they said the military was already bringing in sandbags and moving generators out of basements in low-lying areas. It was also shelving ideas for new construction on flood plains.

Other potential changes include cuts to outdoor training exercises – because of heat waves, or increased weapons maintenance costs and repairs because of heat and dust.

“As we think about changing weather patterns we have to think hard about where operations might be conducted and whether we need to change the assumptions about what kind of air breathing conditions … what kind of sea state we might expect in an operating environment, and what impact they might have.”

The report said troops could also be at greater risk of infectious diseases, which spread more rapidly in hotter temperatures.

Hagel in comments to reporters at the weekend said the Pentagon anticipated an increase in humanitarian missions, because of natural disasters and recurring famines.

He also said the Arctic presented a growing military challenge.

“We see an Arctic that is melting, meaning that most likely a new sea lane will emerge,” he said. “We know that there are significant minerals and natural deposits of oil and natural gas there. That means that nations will compete for those natural resources. That’s never been an issue before. You couldn’t get up there and get anything out of there. We have to manage through what those conditions and new realities are going to bring in the way of potential threats.”

The Pentagon was first instructed by Congress in 2007 to incorporate climate change into its long-term security planning.

But Republicans in Congress have gone on to block the military from preparing for a warmer future, cutting funds for intelligence gathering or testing low-carbon jet fuels.

Officials told the call that planning for the future would help bring down climate-related costs.

“There is a lot you can do to mitigate risk and lower the cost of risks if you acknowledge the risk exists,” the officials said.